Intervalley coupling by quantum dot confinement potentials in monolayer transition metal dichalcogenides

Monolayer transition metal dichalcogenides (TMDs) offer new opportunities for realizing quantum dots (QDs) in the ultimate two-dimensional (2D) limit. Given the rich control possibilities of electron valley pseudospin discovered in the monolayers, this quantum degree of freedom can be a promising carrier of information for potential quantum spintronics exploiting single electrons in TMD QDs. An outstanding issue is to identify the degree of valley hybridization, due to the QD confinement, which may significantly change the valley physics in QDs from its form in the 2D bulk. Here we perform a systematic study of the intervalley coupling by QD confinement potentials on extended TMD monolayers. We find that the intervalley coupling in such geometry is generically weak due to the vanishing amplitude of the electron wavefunction at the QD boundary, and hence valley hybridization shall be well quenched by the much stronger spin-valley coupling in monolayer TMDs and the QDs can well inherit the valley physics of the 2D bulk. We also discover sensitive dependence of intervalley coupling strength on the central position and the lateral length scales of the confinement potentials, which may possibly allow tuning of intervalley coupling by external controlsComment: 17 pages, 14 figure

Building recognition on subregion’s multi-scale gist feature extraction and corresponding columns information based dimensionality reduction

Peer reviewedPublisher PD

Efficient search and comparison algorithms for 3D protein binding site retrieval and structure alignment from large-scale databases

Finding similar 3D structures is crucial for discovering potential structural, evolutionary, and functional relationships among proteins. As the number of known protein structures has dramatically increased, traditional methods can no longer provide the life science community with the adequate informatics capability needed to conduct large-scale and complex analyses. A suite of high-throughput and accurate protein structure search and comparison methods is essential. To meet the needs of the community, we develop several bioinformatics methods for protein binding site comparison and global structure alignment. First, we developed an efficient protein binding site search that is based on extracting geometric features both locally and globally. The main idea of this work was to capture spatial relationships among landmarks of binding site surfaces and bfuild a vocabulary of visual words to represent the characteristics of the surfaces. A vector model was then used to speed up the search of similar surfaces that share similar visual words with the query interface. Second, we developed an approach for accurate protein binding site comparison. Our algorithm provides an accurate binding site alignment by applying a two-level heuristic process which progressively refines alignment results from coarse surface point level to accurate residue atom level. This setting allowed us to explore different combinations of pairs of corresponding residues, thus improving the alignment quality of the binding site surfaces. Finally, we introduced a parallel algorithm for global protein structure alignment. Specifically, to speed up the time-consuming structure alignment process of protein 3D structures, we designed a parallel protein structure alignment framework to exploit the parallelism of Graphics Processing Units (GPUs). As a general-purpose GPU platform, the framework is capable of parallelizing traditional structure alignment algorithms. Our findings can be applied in various research areas, such as prediction of protein inte

Assessment of Cu, Pb and Zn contamination in sediment of north western Peninsular Malaysia by using sediment quality values and different geochemical indices

Surface sediments were collected from the north western aquatic area (13 intertidal sites and 5 river drainages) of Peninsular Malaysia, which were suspected to have received different anthropogenic sources. These sites included town areas, ports, fishing village, industrial areas, highway sides, jetties and some relatively unpolluted sites. The present study revealed that 4.79–32.91 μg/g dry weight for Cu, 15.85–61.56 μg/g dry weight for Pb, and 33.6–317.4 μg/g dry weight for Zn based on 13 intertidal surface sediments while those based on 5 river drainage surface sediments were 10.24–119.6 μg/g dry weight for Cu, 26.7–125.7 μg/g dry weight for Pb and 88.7–484.1 μg/g dry weight for Zn. In general, the metal levels in the drainage sediments are higher than in the intertidal sediments, suggesting dilution factor in the intertidal sediment and direct effluent from point sources in the drainage sediment. In particular, the total concentrations of Cu, Pb, and Zn for the sampling site at Kuala Kurau Town exceeded the Effect Range Median values for Cu, Pb, and Zn for assessments of sediment quality values for freshwater sediment as proposed by MacDonald et al. (Arch Environ Contam Toxicol 39:20–31, 2000), thus adverse biological effects would be observed above this level. Assessment using enrichment factor (using Fe as a normalizer) and geoaccumulation index showed that the three metals at Kuala Kurau Town and Juru Industry drainage were evidenced as having more enrichment and mostly due to non-natural sources. However, caution should be exercised that the interpretation can only become valid when the ratios, indices, and sediment quality values are combined. This is due to the fact that not all the established indices are applicable and, to a certain extent, some of them should be further revised and improved to suit a different metal for Malaysian sediment. Undoubtedly, sites near drainages at Kuala Kurau Town and Juru River Basin need greater attention to mitigate the heavy metal pollution in the future